In a similar incident, a small rock or stone was thrown at the Australian team's bus in September in Chittagong during their two-Test series against Bangladesh.
Jason Behrendorff’s T20I best figures of 4 for 21 handed him Man of the Match award.
The final T20 game will be played in Hyderabad on Friday.
India and Australia will play the final leg of the tour at Hyderabad on October 13.
Australia won the 2nd T20I by 8 wickets against India.
The three T20Is between India and Australia is currently poised at 1-1.
Australia won their first T20I against India since 2012.
Jason Behrendorff and Adam Zampa took 6 wickets between them, conceding a mere 40 runs.
India and Australia are playing the second T20I at Guwahati.